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- PDB-1b87: CRYSTAL STRUCTURE OF AN AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1b87
TitleCRYSTAL STRUCTURE OF AN AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE
ComponentsPROTEIN (AMINOGLYCOSIDE N6'-ACETYLTRANSFERASE TYPE 1)
KeywordsTRANSFERASE / AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE / ANTIBIOTIC RESISTANCE / ACETYL COENZYME A
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Aac(6')-Ii protein
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsWybenga-Groot, L.E. / Berghuis, A.M.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of an aminoglycoside 6'-N-acetyltransferase: defining the GCN5-related N-acetyltransferase superfamily fold.
Authors: Wybenga-Groot, L.E. / Draker, K. / Wright, G.D. / Berghuis, A.M.
History
DepositionFeb 9, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (AMINOGLYCOSIDE N6'-ACETYLTRANSFERASE TYPE 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4122
Polymers20,6021
Non-polymers8101
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (AMINOGLYCOSIDE N6'-ACETYLTRANSFERASE TYPE 1)
hetero molecules

A: PROTEIN (AMINOGLYCOSIDE N6'-ACETYLTRANSFERASE TYPE 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8234
Polymers41,2042
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation26_655-x+1,-y+1/2,z1
Buried area5300 Å2
ΔGint-22 kcal/mol
Surface area17000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)146.960, 146.960, 146.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Cell settingcubic
Space group name H-MI4132

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Components

#1: Protein PROTEIN (AMINOGLYCOSIDE N6'-ACETYLTRANSFERASE TYPE 1) / AAC


Mass: 20602.066 Da / Num. of mol.: 1 / Mutation: VAL127GLU / Source method: isolated from a natural source / Source: (natural) Enterococcus faecium (bacteria) / References: UniProt: Q47764
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 62 %
Crystal growpH: 7.5 / Details: pH 7.5
Components of the solutions
IDNameCrystal-IDSol-ID
1D(+)-SUCROSE11
2(NH4)2SO411
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-10 mg/mlprotein1drop
22 mM1dropAcCoA
35 %(w/v)D(+)-sucrose1drop
40.7 Mammonium sulfate1drop
52.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9809, 0.9795, 0.9792, 0.9770
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 15, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98091
20.97951
30.97921
40.9771
ReflectionResolution: 2.8→40 Å / Num. obs: 6085 / % possible obs: 89.7 % / Redundancy: 2.1 % / Biso Wilson estimate: 19.2 Å2 / Rsym value: 12.7 / Net I/σ(I): 4.3
Reflection shellResolution: 2.8→2.94 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.4 / Rsym value: 33.2 / % possible all: 88.9
Reflection
*PLUS
Rmerge(I) obs: 0.127
Reflection shell
*PLUS
% possible obs: 88.9 % / Rmerge(I) obs: 0.332

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Processing

Software
NameVersionClassification
SOLVEphasing
SHARPphasing
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→40 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.234 825 10.7 %RANDOM
Rwork0.188 ---
obs-7718 99.7 %-
Displacement parametersBiso mean: 11.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.24 Å
Luzzati d res low-40 Å
Luzzati sigma a0.29 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 51 28 1531
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.16
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.211.5
X-RAY DIFFRACTIONx_mcangle_it3.32
X-RAY DIFFRACTIONx_scbond_it4.092
X-RAY DIFFRACTIONx_scangle_it5.512.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 138 11.1 %
Rwork0.245 1109 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2ACO.PARACO.TOP
X-RAY DIFFRACTION3WAT.PARWAT.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.16

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